SNP_29c notebook for Heritability/Association

Author: sarah-ji

docs/heritability.ipynb

@@ -16,24 +16,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "SNP_29C.bed\n",
-      "SNP_29C.bim\n",
-      "SNP_29C.fam\n",
-      "SNP_29C.jld\n",
-      "SNP_29C_results.jld\n",
-      "SNP_29Ctraitdata.csv\n"
+      "SNP_29C_VCM/SNP_29C.bed\n",
+      "SNP_29C_VCM/SNP_29C.bim\n",
+      "SNP_29C_VCM/SNP_29C.fam\n",
+      "SNP_29C_VCM/SNP_29C.jld\n",
+      "SNP_29C_VCM/SNP_29C_results.jld\n",
+      "SNP_29C_VCM/SNP_29Ctraitdata.csv\n"
      ]
     }
    ],
    "source": [
-    ";ls \"SNP_29C*.*\""
+    ";ls \"SNP_29C_VCM/SNP_29C*.*\""
    ]
   },
   {
@@ -100,14 +100,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "  0.551275 seconds (218.60 k allocations: 24.407 MiB, 1.30% gc time)\n"
+      "  0.564255 seconds (219.09 k allocations: 24.571 MiB, 1.00% gc time)\n"
      ]
     },
     {
@@ -142,14 +142,14 @@
        " (true, true)  (true, true)      (false, true)   (false, true) "
       ]
      },
-     "execution_count": 4,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "# read in genotype data from Plink binary file (~50 secs on my laptop)\n",
-    "@time SNP_29C = SnpArray(\"SNP_29C\")"
+    "@time SNP_29C = SnpArray(\"SNP_29C_VCM/SNP_29C\")"
    ]
   },
   {
@@ -444,7 +444,7 @@
     }
    ],
    "source": [
-    "ΦGRM_ped = readcsv(\"kinship_ped29c.csv\", Float64; header = false)"
+    "ΦGRM_ped = readcsv(\"SNP_29C_VCM/kinship_ped29c.csv\", Float64; header = false)"
    ]
   },
   {
@@ -528,7 +528,7 @@
     "using DataFrames\n",
     "\n",
     "SNP_29C_trait = readtable(\n",
-    "    \"SNP_29Ctraitdata.csv\"; header = false,\n",
+    "    \"SNP_29C_VCM/SNP_29Ctraitdata.csv\"; header = false,\n",
     "    separator = ',',\n",
     "    names = [:FID; :IID; :Trait1; :Trait2],  \n",
     "    eltypes = [Int; Int; Float64; Float64]\n",
@@ -1055,7 +1055,7 @@
    "source": [
     "Pkg.add(\"JLD\")\n",
     "using JLD\n",
-    "@save \"SNP_29C.jld\"\n",
+    "@save \"SNP_29C_VCM/SNP_29C.jld\"\n",
     "whos()"
    ]
   },
@@ -1145,7 +1145,7 @@
    "source": [
     "using SnpArrays, JLD, DataFrames, VarianceComponentModels, Plots\n",
     "pyplot()\n",
-    "@load \"SNP_29C.jld\"\n",
+    "@load \"SNP_29C_VCM/SNP_29C.jld\"\n",
     "whos()"
    ]
   },
@@ -1902,7 +1902,7 @@
    ],
    "source": [
     "using JLD\n",
-    "@save \"SNP_29C_results.jld\"\n",
+    "@save \"SNP_29C_VCM/SNP_29C_results.jld\"\n",
     "whos()"
    ]
   },
@@ -1991,7 +1991,7 @@
     }
    ],
    "source": [
-    "SNP_29C_genotypes = readcsv(\"genotypes29c.csv\", Float64; header = false)"
+    "SNP_29C_genotypes = readcsv(\"SNP_29C_VCM/genotypes29c.csv\", Float64; header = false)"
    ]
   },
   {